Turning off Flash/plugins in desktop Safari/Firefox isn't an accurate test. Most sites that cater to the iPhone/iPod Touch use the user-agent string to determine that the user is using one of those devices and then displays the content created for them. The same will, in all likelihood, also be true for the iPad.
YouTube serves H.264 to AppleTV/iPhone/iPod Touch, where H.264 versions are available. They're converting stuff all the time to H.264 so it's not like it's just a little bit of YouTube.
As for the other sites you listed, and the gazillions you didn't: in how many cases is Flash critical to being able to use/enjoy the site? A percentage much smaller than 100, in my experience; certainly not very many in the list you provided. Further, any site who's front page is just a big Flash widget is one that doesn't deserve to be revisited until that particular act of poor design is fixed, but that's just me. It's nice if a Flash plugin is available but you can't reasonably state that it's anywhere near absolutely required to access the majority of Flash-using sites' core functionality.
Sure, Flash is all over the place. Is it absolutely required to nonetheless enjoy surfing the web for several hours a day, for as many days as you want? Not at all.
YouTube serves H.264 to AppleTV/iPhone/iPod Touch, where H.264 versions are available. They're converting stuff all the time to H.264 so it's not like it's just a little bit of YouTube.
As for the other sites you listed, and the gazillions you didn't: in how many cases is Flash critical to being able to use/enjoy the site? A percentage much smaller than 100, in my experience; certainly not very many in the list you provided. Further, any site who's front page is just a big Flash widget is one that doesn't deserve to be revisited until that particular act of poor design is fixed, but that's just me. It's nice if a Flash plugin is available but you can't reasonably state that it's anywhere near absolutely required to access the majority of Flash-using sites' core functionality.
Sure, Flash is all over the place. Is it absolutely required to nonetheless enjoy surfing the web for several hours a day, for as many days as you want? Not at all.
YouTube - Flash based. Yeah yeah yeah, HTML5 beta version, but it's Flash based for now. Apple has a special app for this but you don't get the full YouTube content and functionality, customized pages etc.
Facebook - not Flash based per se, but all the bells and whistles are. Applications, games etc.
MySpace - every damn MySpace page has a flash based music jukebox.
MSN - you'd think Microsoft would favor Silverlight, but anything that moves here is Flash.
Wikipedia - yeah, this one is Flash free.
TV network home pages -- all of'em have streaming content these days that let you watch episodes and clips, all Flash based AFAIK. And it's not just the US ones, every country has a few of these.
These are some of the sites that the mainstream public will most likely visit when they unpack their new shiny iPad, and they will be greeted by blue Lego everywhere. Who cares if these sites will move away from Flash in the coming years? The iPad will start shipping in 50 days. Word of mouth during the initial period will be important as f***, and the word will not be "yup, it's indeed the best way to experience the web", but rather "hey, where'd the web go?"
Steve lingered on the blue Lego long enough to make it clear that he wanted to signal to content providers "in 60 days, make sure these are history". Dream on...